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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
Published on: May 9, 2017
Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap
Philippe Gayral1, José Melo-Ferreira, Sylvain Glémin
1Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.
Plos Genetics
|April 18, 2013
Summary
Population genomics in animals is expanding beyond mammals and drosophilids. This study introduces a reference-free method for analyzing wild species, revealing intermediate genomic diversity patterns and challenging existing vertebrate-invertebrate gaps.
Area of Science:
- Population Genomics
- Metazoan Phylogenetics
- Bioinformatics
Background:
- Population genomic studies are heavily biased towards mammals and drosophilids due to available reference genomes.
- Limited genomic data exists for most metazoan phyla, hindering comparative population genomics.
- Non-model organisms are crucial for understanding broader evolutionary patterns.
Purpose of the Study:
- To develop and apply a de novo, reference-free population genomic analysis pipeline for non-model animal species.
- To investigate population genomic profiles across diverse taxa, including a hare, turtle, oyster, tunicate, and termite.
- To assess the influence of population size on genomic diversity and the non-synonymous to synonymous ratio.
Main Methods:
- Utilized next-generation sequencing transcriptome data from wild-caught individuals.
- Developed a computational pipeline for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning.
- Incorporated specific strategies for hidden paralogy detection in reference-free analyses.
Main Results:
- Successfully performed de novo population genomic analysis in five non-model species.
- Demonstrated the robustness of reference-free inferences by comparing results with reference-guided analyses in two species.
- Found population genomic profiles intermediate between human and Drosophila, suggesting no generalized vertebrate-invertebrate gap.
- Observed higher average genetic diversity in invertebrates than vertebrates (except termite), correlating with larger population sizes.
- Identified a negative correlation between genetic diversity and the non-synonymous to synonymous ratio within vertebrates and invertebrates.
Conclusions:
- The developed pipeline enables robust genome-wide population analyses in non-model organisms without reference genomes.
- The findings challenge the notion of a broad genomic diversity gap between vertebrates and invertebrates.
- Population size appears to be a significant factor influencing both overall genetic diversity and the ratio of non-synonymous to synonymous substitutions.
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